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PubMed2004

Comparative genomic analysis as a tool for biological discovery.

The recent completion of the human genome sequence has enabled the identification of a large fraction of our gene catalogue and their physical chromosomal position. However, current efforts lag at defining the cis-regulatory sequences that control the spatial and temporal patterns of each gene's expression. This task remains difficult due to our lack of knowledge of the vocabulary controlling gene regulation and the vast genomic search space, with greater than 95% of our genome being noncoding. Recent comparative genomic-based strategies are beginning to aid in the identification of functional sequences based on their high levels of evolutionary conservation. This has proven successful for comparisons between closely related species such as human-primate or human-mouse, but also holds true for distant evolutionary comparisons, such as human-fish or human-bird. In this review we provide support for the utility of cross-species sequence comparisons by illustrating several applications of this strategy, including the identification of new genes and functional non-coding sequences. We also discuss emerging concepts as this field matures, such as how to properly select which species for comparison, which may differ significantly between independent studies.

Animals↗
PubMed2006

Proteomic analysis of malignant ovarian cancer effusions as a tool for biologic and prognostic profiling.

PURPOSE: Malignant epithelial ovarian cancer effusions are important in disease dissemination and clinical outcome. The identification of biochemical events active in effusions may improve our identification and application of targeted therapeutics. EXPERIMENTAL DESIGN: Archival effusion samples for which outcome information was known were studied. Clinical variables were comparable between these groups. Two cohorts of patients with malignant effusion were assessed: those with effusion at presentation (Tap1) or at first recurrence (Tap2). Expression and activated fraction of selected signaling proteins were quantitated on serial protein microarrays using validated antibodies. Proteomic results and clinical variables were analyzed by univariate analysis followed by Cox proportional hazards model analysis. RESULTS: Malignant effusions (>80% malignant cells) were distinguished from benign effusions by higher expression of AKT, activated extracellular signal-regulated kinase, activated (P < or = 0.001) and total cAMP-responsive element binding protein (P = 0.01), and JNK (P = 0.03). Malignant pleural effusions could not be differentiated from ascites by signaling profiles. Both had signal expression clusters for survival, proliferation and metastasis, and injury pathways. Cox proportional hazards model analysis revealed high p38 and pEGFR/EGFR ratio as jointly associated with poor survival in Tap1 cases (both P < or = 0.002). Phospho-JNK quantity was associated with worse outcome in Tap2 patients (P = 0.004), when taking other factors into consideration. CONCLUSIONS: Proliferation, survival, and apoptosis signaling dysregulation can be identified in ovarian cancer effusion samples. Biochemical characterization of clinical effusions may provide either predictive and/or correlative information on patient outcome from which to further understand the mechanisms of effusion development and target clinical intervention.

Apoptosis↗
PubMed2004

High resolution imaging as a characterization tool for biological crystals.

Biomolecular crystals consist of large unit cells that form a rather flexible medium that is able to accommodate a certain degree of lattice distortion, leading to several interesting issues ranging from structural to physical properties. Several techniques, from X-ray diffraction to microscopy, have been adapted to study the structural and physical properties of biomolecular crystals systematically. The use of synchrotron-based monochromatic X-ray diffraction topography, with triple axis diffractometry and rocking curve measurements, to characterize biomolecular crystals is reviewed. Recent X-ray diffraction images from gel and solution grown lysozyme crystals are presented. Defect structures in these crystals are discussed, together with reciprocal space mapping, and compared with results obtained from crystals grown in a low gravity environment.

Animals↗
PubMed2000

PepTool and GeneTool: platform-independent tools for biological sequence analysis.

Although we are unable to discuss all of the functionality available in PepTool and GeneTool, it should be evident from this brief review that both packages offer a great deal in terms of functionality and ease-of-use. Furthermore, a number of useful innovations including platform-independent GUI design, networked parallelism, direct internet connectivity, database compression, and a variety of enhanced or improved algorithms should make these two programs particularly useful in the rapidly changing world of biological sequence analysis. More complete descriptions of the programs, algorithms and operation of PepTool and GeneTool are available on the BioTools web site (www.biotools.com), in the associated program user manuals and in the on-line Help pages.

Amino Acid Sequence↗
PubMed2005

Water-soluble hybrid nanoclusters with extra bright and photostable emissions: a new tool for biological imaging.

We report the generation of a previously unknown class of water-soluble organic-inorganic hybrid nanoclusters composed of silver and thioflavin T with remarkable fluorescent properties. These hybrid nanoclusters display an extra bright fluorescence in aqueous solutions without any detectable photobleaching. Furthermore, the fluorescent nanoclusters can be generated in situ by sensitized photoreduction of Ag+. Organic-inorganic nanoclusters have remarkable advantages over the known classes of fluorescent probes for the development of ultrasensitive biological assays, cell imaging, or studies of single molecules. As an example of a practical biological application, imaging of amyloid fibrils produced from recombinant mammalian prion proteins and nonprion proteins using hybrid nanoclusters is presented.

Amyloid↗
PubMed2002

Detection of single-strand breaks and base damage in DNA of human white blood cells as a tool for biological dosimetry of exposure to ionizing radiation.

An immunochemical assay has been adapted to detect DNA damage in whole blood at biologically relevant doses of ionizing radiation. Upon alkaline treatment of whole blood, both strand breaks and base damage (which is converted into strand breaks by the addition of damage-specific enzymes) are detected by using antibodies that specifically bind to single-strand DNA. Single-strand breaks can be detected immediately after irradiation at doses as low as 0.2 Gy. With unknown background damage, the lower detection limit increased to approximately 0.5 Gy immediately after irradiation due to interindividual variation. Because single-strand breaks are repaired rapidly, this method is suitable only for blood collected less than 1 hour after exposure. Base damage represents a very promising biological indicator that can be used 1 hour and longer (at least to 4 hours) after radiation exposure because of an apparent lack of base damage repair during this time window.

DNA↗